I never had any answers, but I was just curious not stuck.
At 3V, you really need to charge the 12V battery. I believe all the computers run on 12V; I think you should see the display etc. come on with a good charge in it even if your HV battery is really dead. You should be able to jump-start it from another vehicle, or motorbike - only problem is that a regular
jump cable clips are too big and you risk shorting something out in the fusebox; I bought a bike set for emergency use.
If the display comes up, you can check the 12V voltage in diagnostic mode (hold down INFO and
turn the tail lights on and off a few times, then select "vehicle signals" or some such)
Re. battery replacement, it's probably not worth trying to save money getting a Harley battery or whatever. It's shoehorned in pretty good, has
funny connectors and a vent pipe - http://andrew.triumf.ca/andrew/prius/12battery2.jpg
But maybe you can find a compatible OEM battery from a specialist store.